Running the spades.py command on the cleaned "Day 2" datasets.
Match this to your CPU's physical cores to speed up the process (e.g., -t 4 ). 3. Focus on Scaffolds vs. Contigs SPADES-Day2-pc.rar
Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta . Running the spades
spades.py --careful -1 reads_1.fastq.gz -2 reads_2.fastq.gz -o day2_output 2. Monitor Resource Allocation SPADES-Day2-pc.rar
SPAdes is known for being extremely memory-intensive. A useful practice during "Day 2" exercises is explicitly limiting its resource usage to prevent your PC from crashing.
Without it, your final sequence might have small errors that make downstream analysis (like finding genes) more difficult.